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Hi
I use square brackets for my notes, not for aesthetical reasons but for practical ones. With them, I can click on the links on any ePub, less so when I keep only a plain number (well, clicking ability improves with the number of digits).
When I produce an ePub, I usually add square brackets using this joint regex with the Calibre editor (written in .json format, you can import it). Most probably, you can achieve a similar result with Sigil. You could adapt it so that to make it work in reverse order (i.e. to suppress all unwanted square brackets in one go ). Anyway you certainly do not need to do that manually...
Admittedly, a Preference setting giving the user an alternative choice of using or not square brackets would be quite nice, but I have no idea on how difficult it would be to implement...
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